The 'computer' is probably a Mopar Performance ECU. John had a good source on those. What's it do? Biggest benefit on a car with no cats is that it has no rear O2 sensing. This not only keeps the check engine light off, it also maintains the correct A/F mixture (as it does when the stock ECU is used and it is getting nominal voltages from the rear sensors) When the stock ECU doesn't get the proper voltages from the rear O2 sensors and it won't when the CATS are off, the ECU richens the A/F mixture and the car runs rich. This results in robbing the car of a little HP but more importantly, in causing the car to 'blubber' on idle.
I'd check to see if the car has CATS. If it does, the Mopar ECU, IMHO, is not of much benefit. The CATS are in the side sills...
Also, if the car doesn't have the CATS with it, you should know that they are expensive to replace. The dealer may be unaware of whether the CATS are on it or not. I'd make'em check.
Nothing wrong with Hennessey headers or tubes.
Biggest difference between '99 and '01 Vipers?
ABS on the '01 - Good
Forged Pistons on the '99 - Good
There's my opinion. Good luck.